Research for analysis of genetic information of various organisms is now under progress. A great number of genes including those of human, the base sequences thereof, proteins coded by the gene sequences, and sugar chains produced secondary from these proteins are now being elucidated quite rapidly. The functions of the genes, proteins, and sugar chains with known sequence can be studied by various methods. Nucleic acids, and their relationship with various genes and biological functions, can be studied by using various nucleic acid/nucleic acid complementarity, for example by Northern or Southern blotting. The function and expression of proteins can be studied by using protein/protein reactions, for example by western blotting.
A new analytical method called DNA-microarray method (DNA chip method) was developed recently as a method of analyzing expression of multiple genes simultaneously and is attracting attention. These methods are in principle the same as conventional methods in that they are the nucleic acid detecting and quantitative determining method based on nucleic acid/nucleic acid hybridization reaction. These methods are applicable to the methods of detecting and quantitatively determining proteins and sugar chains, based on specific protein/protein, sugar chain/sugar chain, or sugar chain/protein interaction. These methods are characteristic in that a planar glass substrate called microarray or DNA chip carrying multiple DNA fragments, proteins, and sugar chains immobilized thereon orderly at high density is used. Typical examples of the DNA chip method includes a method of hybridizing, for example, an expression gene in the cell under investigation with a fluorescent dye-labeled sample on a planar substrate, allowing complementary nucleic acids (DNA or RNA) to bind to each other, and scanning the reaction sites with a high-definition detection device (scanner) at high speed, and a method of detecting a response, for example in electric current, based on electrochemical reaction. In this manner, it is possible to estimate the amount of a particular gene in sample rapidly. Application of the DNA chip is not limited to gene expression analysis of estimating the amount of expressed gene, and it is highly expected as a means to detect single nucleotide polymorphism (SNP).
For example, a method of coating a flat substrate such as slide glass with poly-L-lysine, aminosilane, or the like and immobilizing nucleic acids by using a spotting device called spotter was developed as a method of immobilizing a nucleic acid on substrate (Published Japanese Patent Application No. 10-503841).
cDNAs and the fragments thereof having hundreds to thousands of bases, which were used traditionally as the nucleic acid probe (nucleic acid immobilized on substrate) for use in DNA chip, are being replaced gradually by oligo DNAs (oligo DNAs are DNAs having a base number of 10 to 100), because oligo DNAs reduce the error during hybridization with analyte and are easily prepared in synthesizer. The oligo DNAs are bound to the glass plate covalently (Published Japanese Patent Application No. 2001-108683).
Currently, DNA chips are mainly used as a research tool for analyzing a great number of genes at once by placing from tens of thousands of to several thousand of genes on a single chip. It is hoped that DNA chips will be used more widely in diagnostic applications. Generally when the DNA chip is used in diagnostic application, it is predicted that the amount of the sample collected would be very small. Current DNA chips are still insufficient in sensitivity, and thus, it would be impossible to analyze such a sample. In addition, with a current DNA chip, the fluorescence intensity of genes lower in expression amount after hybridization is very low, and thus, the current DNA chips still have a problem that it is practically impossible to analyze such genes. Accordingly, current DNA chips have a problem that how to increase the fluorescent intensity after hybridization of the samples lower in quantity and genes lower in expression amount. To solve the problem above, it is critical to improve the efficiency of the reaction between the analyte DNA and the probe DNA. For acceleration of the reaction between analyte DNA and probe, natural diffusion of the analyte is insufficient, and it is thought that accelerating the reaction between probe and analyte efficiently by stirring the solution.
For example as a method of stirring an analyte solution, Published Japanese Patent Application Nos. 2003-248008 and 2003-339375 disclose a method of increasing the reaction efficiency with an analyte by agitating an analyte solution while moving magnetic beads in the analyte solution by magnetic force. Alternatively, Published Japanese Patent Application No. 2003-339375 discloses a method of increasing the signal after hybridization, by bringing an analyte solution containing beads into contact with a DNA chip, sealing the solution, for example, with a cover glass, forcing the beads to drop in the gravitational direction while rotating the chip, and thus agitating the analyte solution.
However, the methods described in Published Japanese Patent Application Nos. 2003-248008 and 2003-339375 still had the following problems.
That is, generally when an analyte solution is sealed with a common cover glass on a flat plate-shaped DNA chip, the clearance between the cover glass and the DNA chip is approximately 10 μm at most. Thus, it caused a problem that fine particles larger in diameter than the clearance, when added, are held in the clearance between the DNA chip and the cover, prohibiting movement of the fine particles and making the stirring ineffective. In addition, use of fine particles of several μm in diameter, caused a problem that the fine particles do not move in the analyte solution efficiently because of the solution resistance even if forced by gravity or the like, resulting in insufficient stirring. Contact of the fine particles with the DNA probe-immobilized carrier seems to be one reason for insufficient characteristic of stirring even the migration of the fine particles is forced by gravity. Alternatively, the solution may be stirred by agitating the fine particles in the reaction solution, by expanding the clearance between the cover glass and the DNA chip for example with an O-ring, increasing the size of the agitating fine particles, and forcing the movement of the particles by gravitational or magnetic force. However, the cover glass and the DNA chip are both flat in shape for sealing, and thus, the fine particles move through the DNA probe-immobilized region. As a result, the fine particles often damaged the probe DNA-immobilized region, causing problems such as difficulty of data analysis and decrease in signal intensity because of separation of the probe by collision of the fine particles to the probe-immobilized surface.